Using massively-paralleled sequencing to find the cause of inherited conditions that affect the front of the eye

Project description

Eye diseases are a common cause of human disability and many of them are inherited. These include congenital as well as adult-onset conditions and diseases of ageing, and may involve abnormalities at the back of the eye or the anterior eye structures. We are currently working on a range of eye diseases that affect the front of the eye including primary glaucoma (eg. Ali et al 2009, Am J Hum Genet 84, 664-671), cataracts (eg. Khan et al 2011, Am J Hum Genet 89, 464-473), corneal dystrophies (eg. Siddiqui et al 2014, Cornea 33:247-51), keratoconus and strabismus. A major strength is our access to patients and patient samples through links with local clinicians. We also benefit from many national and international collaborations, and the group now manages unique cohorts of patients’ DNA and cells. Ultimately it is hoped that genetic analyses of these patients will contribute to the search for cures for both rare and common inherited human eye diseases.

The projects offered involve studying the molecular basis of these potentially blinding conditions in families with multiple affected members. To search for the pathogenic mutation(s), the student will prepare and analyse next-generation sequencing data using the established pipeline. To identify the genes and proteins involved they may also use a combination of autozygosity mapping, genotyping, bioinformatic analysis and Sanger DNA sequencing. Once the mutation has been identified, there will also be the opportunity to perform a range of molecular and cell biological techniques to characterise the mutant protein and determine the function of the normal protein during eye development. These experiments will involve reverse transcription PCR, in situ hybridisation, immunohistochemistry, siRNA (for gene knock-down) and molecular cloning with cell biology (for over-expression studies).

Entry requirements

This project is available immediately to both Home/EU rate applicants and International applicants who are able to self-fund their studies. Students must be able to provide the appropriate level of fees based on their fee status plus laboratory consumables costs per year. This is in addition to the provision of personal living expenses.

You should hold a first degree equivalent to at least a UK upper second class honours degree in a relevant subject. 

Candidates whose first language is not English must provide evidence that their English language is sufficient to meet the specific demands of their study, the Faculty minimum requirements are:

  • British Council IELTS - score of 6.5 overall, with no element less than 6.0.
  • TOEFL iBT - overall score of 92 with the listening and reading element no less than 21, writing element no less than 22 and the speaking element no less than 23.

How to apply

Applications can be made at any time. Potential applicants should initially contact the lead supervisor Dr Manir Ali at with enquiries about this research project.

To formally apply for this project applicants should complete a Faculty Scholarship Application form and send this alongside a full academic CV, degree transcripts (or marks so far if still studying) and degree certificates to the Faculty Graduate School

We also require 2 academic references to support your application. Please ask your referees to send these references on your behalf, directly by email

If you have already applied for other scholarships using the Faculty Scholarship Application form you do not need to complete this form again. Instead, you should email to inform us you would like to be considered for this scholarship project.